Size matters: point pattern analysis biases the estimation of spatial properties of stomata distribution

Using quantitative methods to understand leaf epidermal development

As the interface between plants and the environment, the leaf epidermis provides the first layer of protection against drought, ultraviolet light, and pathogen attack. This cell layer comprises highly coordinated and specialised cells such as stomata, pavement cells and trichomes. While much has been learned from the genetic dissection of stomatal, trichome and pavement cell formation, emerging methods in quantitative measurements that monitor cellular or tissue dynamics will allow us to further investigate cell state transitions and fate determination in leaf epidermal development. In this review, we introduce the formation of epidermal cell types in Arabidopsis and provide examples of quantitative tools to describe phenotypes in leaf research. We further focus on cellular factors involved in triggering cell fates and their quantitative measurements in mechanistic studies and biological patterning. A comprehensive understanding of how a functional leaf epidermis develops will advance the breeding of crops with improved stress tolerance.

A systems genetics approach to deciphering the effect of dosage variation on leaf morphology in Populus

Gene copy number variation is frequent in plant genomes of various species, but the impact of such gene dosage variation on morphological traits is poorly understood. We used a large population of Populus carrying genomically characterized insertions and deletions across the genome to systematically assay the effect of gene dosage variation on a suite of leaf morphology traits. A systems genetics approach was used to integrate insertion and deletion locations, leaf morphology phenotypes, gene expression, and transcriptional network data, to provide an overview of how gene dosage influences morphology. Dosage-sensitive genomic regions were identified that influenced individual or pleiotropic morphological traits. We also identified cis-expression quantitative trait loci (QTL) within these dosage QTL regions, a subset of which modulated trans-expression QTL as well. Integration of data types within a gene co-expression framework identified co-expressed gene modules that are dosage sensitive, enriched for dosage expression QTL, and associated with morphological traits. Functional description of these modules linked dosage-sensitive morphological variation to specific cellular processes, as well as candidate regulatory genes. Together, these results show that gene dosage variation can influence morphological variation through complex changes in gene expression, and suggest that frequently occurring gene dosage variation has the potential to likewise influence quantitative traits in nature.

Spatial modeling of biological patterns shows multiscale organization of Arabidopsis thaliana heterochromatin

The spatial organization in the cell nucleus is tightly linked to genome functions such as gene regulation. Similarly, specific spatial arrangements of biological components such as macromolecular complexes, organelles and cells are involved in many biological functions. Spatial interactions among elementary components of biological systems define their relative positioning and are key determinants of spatial patterns. However, biological variability and the lack of appropriate spatial statistical methods and models limit our current ability to analyze these interactions. Here, we developed a framework to dissect spatial interactions and organization principles by combining unbiased statistical tests, multiple spatial descriptors and new spatial models. We used plant constitutive heterochromatin as a model system to demonstrate the potential of our framework. Our results challenge the common view of a peripheral organization of chromocenters, showing that chromocenters are arranged along both radial and lateral directions in the nuclear space and obey a multiscale organization with scale-dependent antagonistic effects. The proposed generic framework will be useful to identify determinants of spatial organizations and to question their interplay with biological functions.

Automatic Stomatal Segmentation Based on Delaunay-Rayleigh Frequency Distance

The CO₂ and water vapor exchange between leaf and atmosphere are relevant for plant physiology. This process is done through the stomata. These structures are fundamental in the study of plants since their properties are linked to the evolutionary process of the plant, as well as its environmental and phytohormonal conditions. Stomatal detection is a complex task due to the noise and morphology of the microscopic images. Although in recent years segmentation algorithms have been developed that automate this process, they all use techniques that explore chromatic characteristics. This research explores a unique feature in plants, which corresponds to the stomatal spatial distribution within the leaf structure. Unlike segmentation techniques based on deep learning tools, we emphasize the search for an optimal threshold level, so that a high percentage of stomata can be detected, independent of the size and shape of the stomata. This last feature has not been reported in the literature, except for those results of geometric structure formation in the salt formation and other biological formations.